GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacJ in Desulfacinum infernum DSM 9756

Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_073037934.1 BUB04_RS06025 ABC transporter ATP-binding protein

Query= uniprot:D4GP38
         (383 letters)



>NCBI__GCF_900129305.1:WP_073037934.1
          Length = 365

 Score =  262 bits (669), Expect = 1e-74
 Identities = 153/362 (42%), Positives = 214/362 (59%), Gaps = 23/362 (6%)

Query: 3   QIQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYI 62
           QI++ D+ K +G   AV  +S  +++ + LV++GPSGCGK+T LR++AGLE  TSG I+I
Sbjct: 2   QIEIRDVRKDYGRVQAVRGVSFSVEEGQLLVILGPSGCGKTTLLRLIAGLEPVTSGTIHI 61

Query: 63  GGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETL 122
            G  + +  P  R+I+MVFQ YAL+PH+ VR+NI FGL+  +   + E + R+  V + L
Sbjct: 62  AGTDVTHLPPVKRNISMVFQSYALFPHLNVRENIIFGLKVRK-VPADEIERRLKRVVDLL 120

Query: 123 GIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQD 182
           G++  LD KP ELSGG QQRVALGRAI+ +  V LMDEPLSNLDAKLR  MR E+ +LQ 
Sbjct: 121 GLSGRLDSKPGELSGGMQQRVALGRAIIAEKPVTLMDEPLSNLDAKLRNSMRREICSLQR 180

Query: 183 QLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMINL 242
           +L +T +YVTH+Q EAMTMADRI +M DG++ Q  SP   Y  P N FVA FIG P +N+
Sbjct: 181 RLGITMIYVTHDQVEAMTMADRIVLMRDGQIVQDDSPENFYERPANTFVARFIGTPPMNI 240

Query: 243 VRGTRSESTFVGEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVADAAPDDAALDDHDLQ 302
           V    ++     E     L   +     D D ++ G+RPE++ +A++           L 
Sbjct: 241 VPLCPTQGGAALEPGGRLLFPGM-----DPDRYLFGIRPENLRLAESGQPAMVTGREYLG 295

Query: 303 MDVTV-VEPHGDQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTVTIPPDKIHLFDA 361
            D  V  E HG + ++                 T G   +  G  V +T  P  ++LFDA
Sbjct: 296 SDTFVSCEIHGQEVIVR----------------TRGRRNIREGTVVHLTWDPGDVNLFDA 339

Query: 362 ET 363
            T
Sbjct: 340 RT 341


Lambda     K      H
   0.317    0.135    0.386 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 344
Number of extensions: 14
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 383
Length of database: 365
Length adjustment: 30
Effective length of query: 353
Effective length of database: 335
Effective search space:   118255
Effective search space used:   118255
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory